This is way off topic but you've made a number of assertions that needs to be addressed. For example, you say that I leave out various homologies. But in fact, I don't, the homologies you cite strengthen the fact that there exist mini-IC systems that would require unselectable steps for any evolutionary pathway.

"Mini-IC systems?" But I thought that IC meant that the *whole thing* was IC?

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For example, with regard to MotAB, the motor complex in the flagellum requires 3 components, fliG, motA, and motB, and this is analogous to the ICness of ExbB, ExbD, and TonB.

ExbB and ExbD act on TonB, IIRC there's another ExbBD pair homolog that acts on something else. And motAB act on fliG in a similar fashion. Which is why Kojima & Blair wrote in Biochemistry (2001, vol. 40, pp. 13041-50),

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The occurrence of significant conformational change in the stator has implications not only for the present-day mechanism but also for the evolution of the flagellar motor. A membrane complex that undergoes proton-driven conformational changes could perform useful work in contexts other than (and simpler than) the flagellar motor, and ancestral forms of the MotA/MotB complex might have arisen independently of any part of the rotor.

Nelson continues,

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Still, there are more problems with regard to the logistical operations needed to be performed by a stochastic process in order to make this thing work from an ion channel, as Mike points out:

quote:--------------------------------------------------Of all the ways to mutate an ion channel, the number of ways that would result in its interacting with the base of some filament is surely in the distinct minority. And of all the ways to mutate an ion channel that gloms onto a filament, the number of ways to mutate it such that rotation does not occur is probably much higher than the number of ways to elicit some rotation...

None of this is disputed, but all it is saying is that "beneficial mutations are unlikely" which is no surprise to evolutionary biology. All that is needed is one rare beneficial mutation amongst millions of ones that "don't work" and selection will pick it out. And, FWIW, mutation experiments seem to indicate that there is a fair bit of flexibility where motor function is retained despite mutation in the MotB--rotor interface.

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This [mutation] allows some ion channel to glom onto the base of a filament and open its channel and expose the ion flow to the proto-rotor in such a way that a set of electrostatic interactions just happen to form and elicit significant rotation.

This depends upon a particular model of the mechanism of flagellar rotation, which is an unsolved question (Hey! A place for the IDer to act in modern times! Unless you're a nasty methodological naturalist...). Based on the ExbBD homology, I would expect that the ion channel is essentially internal to the ExbBD system and that the energy resulting from H+ flow is transferred through the protein structure via conformational change to act on the flagellum base (or on TolB etc.) to do work at a distance. Call it a prediction if you like. The electrostatic model certainly is elegant, but based on ExbBD homologs being independent units doing "work at a distance" in several different systems, it seems unlikely. Time will tell.

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The homology between FliI is said to only be homologous to the b subunit of the F-ATP synthase, not the whole 8 parts of the synthase, the whole thing requires all 8 parts to work.

IIRC the 3 alpha and 3 beta subunits of the F1 ATPase are thought to be homologs of each other, with only the beta subunits retaining ATPase activity:

The similarity of the beta subunit to FliI is something like 33% which is highly statistically significant, well above the ambiguous level:

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How might these ATPases catalyze processive protein export? Spa47 (the Shigella FliI homolog) shares 33% amino acid identity with the beta-subunit of F1-ATPase. Proteins with >30% sequence identity have a high probability of sharing similar structures (69). Active F1-ATPase is a heterohexamer consisting of alternating alpha- and beta-subunits with a gamma-subunit inserted in a central channel where it rotates during the catalytic cycle (70). No equivalent of the alpha-subunit of F1-ATPases is found within flagellar or TTSS-encoding operons, so we assume that the type III export motor is a homohexamer. When modeled on the F1 structure, Spa47 fits at the inner membrane base of our NC structure (Fig. 3). It would contain a central channel aligned with the one found within the NC and of similar diameter to it, through which the proteins could be secreted (see Supporting Text).

...the assumption of homology seems to be confirmed by the fact that the resulting protein complex fits well into their model of T3SS structure.

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With respect to the possibility that the rod proteins were derived from each other, Mike Gene addresses this in his essay:

quote:--------------------------------------------------It would seem there is no reason why the rod should be built around three proteins instead of simply one. Yet these three gene products are found in all flagella, dating back to the putative ancestral flagellum. This suggests one protein is not sufficient to form a functioning flagellar rod. Furthermore, the size of these proteins among these five distantly related bacteria has been held relatively constant (Fig 2), despite billions of years of experiencing very different selective pressures. It would seem some form of constraint or specification is at work, as natural selection will not tolerate too much deviation. And these size constraints map back to the last common ancestral flagellum, indistinguishable from the first flagellum.

It seems highly unlikely that the different rod proteins have radically different functions. Probably their retention has to do with starting and stopping the rod construction process, wherein it would be helpful to have a tightly-controlled starting and stopping points, but where simpler mechanisms could suffice at first, e.g. just generating a certain amount of one rod protein.

All that is required to get from one rod protein to several is the sub-functionalization of gene copies, which you, Nelson, have enthusiastically endorsed in other threads.

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Gram positive bacteria don't need the L and P rings because they simply do not have an outer membrane. I think that it's as simple as that (well not really, Mike has hinted at how this can illuminate something about it's origin but hasn't discussed this yet).

So, are they part of the IC system or not, and how many orders of magnitude difference in probability does this decision result in?

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I'm not familiar with a flagellum serving as an adhesion organelle, although I'm familiar with pili that do.

With that you continue to introduce more unselectable steps, the irreducible complexity of the folding of P Pilus, not to mention the sophisticated mechanisms, donor strand exchange and donor strand complementation. The pilus itself is made up of 5 parts, PapK PapA,PapE,PapK, and PapG. Furthermore, the pilus doesn't seem to be able to secrete proteins, and the biggest difference between flagella and pili is that flagella are built from the top to the bottom, whereas pili are built from the bottom to the top. The notion of a simple filament sticking to an export machine seems to vanish.

Huh? There are many kinds of pili, the term basically means "sticky-outy bit" as far as I can tell. And it seems that basically every transport system that has been identified has versions that support extracellular extensions. They all have to secrete proteins, in order to get the pilus proteins to the outside. You are focusing on the abilities of the P pilus, built on a Type I transporter IIRC, but we are talking about type III secretion systems. It appears that flagella and pili can be built from the top or the bottom, since Type III and Type IV (both have motile flagella and nonmotile pili systems) do each respectively.

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As far as the last two, I would need to see those for myself. I am cautious at Nic's constant mentioning of homology due to the fact that he doesn't take anything like convergence or coincidence (or common design) into account, which kind of makes me careful to accept his criteria for saying something is homologous. And as we have seen, structural homologies are not good indicators of common descent.

Sequence and structural homology are well-documented concepts with a great deal of predictive theory and evidence behind them. "Common design" is the at-random invocation of "the designer would have put statistically significant but functionally pointless similarities in a phylogenetic pattern for no good reason" which is erected as a smoke screen to avoid dealing with the statistically significant but functionally unnecessary similarity.

For the chemotaxis homologs, see this thread. The similarites are in sequence, not just structure IIRC.

As for the secretin, the evidence is merely suggestive at this point: there is no statistical evidence of homology at this point AFAIK. But it is interesting that the outer membrane ring of flagella is secreted by a type II rather than type III pathway, as is the secretin used in the outer membrane of type III virulence systems, as is the outer membrane secretin used in a large number of other transport systems (see: Bitter W., Secretins of Pseudomonas aeruginosa: large holes in the outer membrane. Arch Microbiol 2003 May;179(5):307-14). If structural homology is discovered at some point, then another piece of the puzzle will have fallen into place.

Even here we are a far cry from Dembski's strawman of getting flagellum parts from the mythical, mystical "protein supermarket".

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As Mike Gene states, as far as pores go, not any old pore would do. The logic of this is that with all the pores that exist, if things were that simple, we should see plasticity among flagella of eubacteria (indeed this is one of the major problems with co-option stories, no plasticity.)

I'm not sure what the logic is. The point is not plasticity in eubacterial flagella (although there is some of that), the point should be that several different complex motility systems are based on several different transport systems. Assuming that the eubacterial flagella was "the goal" is unwarranted (a form of "painting the target around the arrow"), because we have archaeal flagella, twitching motility, slime-secretion motility, and probably other systems. It appears that something like half of the classes of secretion systems have the capability to be modified to make use of their "sticky-outy bits" for motility. Evolutionary theory doesn't need to postulate that "any old pore" would do, just that there are a lot of different pores, and that some of them would do.